xmipp3.protocols.protocol_projmatch.protocol_projmatch module

class xmipp3.protocols.protocol_projmatch.protocol_projmatch.XmippProtProjMatch(**args)[source]

Bases: pwem.protocols.protocol_3d.ProtRefine3D, pwem.protocols.protocol_3d.ProtClassify3D

3D reconstruction and classification using multireference projection matching

FILENAMENUMBERLENGTH = 6
allCtfGroups()[source]

Iterate over all CTF groups.

allIters()[source]

Iterate over all iterations.

allRefs()[source]

Iterate over all references.

angularProjectLibraryStep(iterN, refN, args, stepParams, **kwargs)[source]
assignImagesToReferencesStep(iterN)[source]
calculateDeviationsStep(it)[source]

Calculate both angles and shifts devitations for all iterations

calculateFscStep(iterN, refN, args, constantToAdd, **kwargs)[source]
cleanVolumeStep(vol1, vol2)[source]
convertInputStep()[source]

Generated the input particles metadata expected by projection matching. And copy the generated file to be used as initial docfile for further iterations.

createIterDirsStep(iterN)[source]

Create the necessary directory for a given iteration.

createOutputStep()[source]
executeCtfGroupsStep(**kwargs)[source]
filterVolumeStep(iterN, refN, constantToAddToFiltration, **kwargs)[source]
getLastIter()[source]
initAngularReferenceFileStep()[source]
itersBoolValues(attributeName, firstValue=False)[source]

Take the string of a given attribute and create a list of booleans that will be used by the iteratioins. An special first value will be added to the list for iteration 0.

itersFloatValues(attributeName, firstValue=-1)[source]

Take the string of a given attribute and create a list of floats that will be used by the iteratioins. An special first value will be added to the list for iteration 0.

itersStringValues(attributeName, firstValue='c1')[source]

Take the string of a given attribute and create a list of strings that will be used by the iteratioins. An special first value will be added to the list for iteration 0.

projectionMatchingStep(iterN, refN, args)[source]
reconstructionStep(iterN, refN, program, method, args, suffix, **kwargs)[source]
storeResolutionStep(resolIterMd, resolIterMaxMd, sampling)[source]
transformMaskStep(program, args, **kwargs)[source]
volumeConvertStep(reconstructedFilteredVolume, maskedFileName)[source]